Shadow Lugia: the Fallen Gaurdian of the Sea
by Endevorer
Summary: Ash, Misty, Brock, May, Max, and Team GoGetters along with Michael and Jovi are caught in the battle to stop Cipher and Purify Shadow Lugia. Mean while, many family secrets are revealed.
1. Prolouge

First and Last disclaimer for entire fic: I don't own Pokemon. And the Apprentice system belongs to a dead guy who I don't know.

A/N: I edited this chapter from the original I made, fixed some errors and added more depth into the characters. Personally, I think I went a little darker than what I originally had.

There are several AUs also, such as Jovi coming with Michael to stop Cipher.

* * *

A red haired boy, about ten or so, anxiously stood next to an elevator, waiting for something. He wore a yellow jacket and had a strange device around his left arm. Its chrome exterior fit perfectly well in the sci-fi room he was in. He waited patiently, hoping he wasn't too late. Just then he heard foot steps coming from behind him, as a younger girl, a Plusle and Minun perched both her shoulders, quickly dashed towards him. "Jovi, you're late!" The boy told the girl.

"Sorry Michael, Jovi will be faster next time." The girl, now identified as Jovi, told the older boy. Jovi, even though she was smarter than most people, always addressed herself in third person. She wore a white skirt. Around her arm was the same device on Michael's arm. "Jovi ready for Greevil!" She cried with both anxiety and joy, like Christmas had come early and Santa was having dinner with her. She was so innocent and sweet; it was a crime that she had to be involved with Cipher and the Shadow Pokemon. Yet she wasn't affected by the idea of stealing Pokemon to purify and set free.

Michael inhaled and exhaled, trying to focus his mind towards this particular battle. This battle was for all the marbles, the one final turning point in a war. He made his way towards the elevator, ready for what could be the biggest moment in his young life. The glass door opened and he walked into the tube. Jovi and her Pokemon sighed in unison, all three of them knowing that it wasn't the time for childish thoughts. As she stepped in, Michael pushed a button on the nearby elevator console and the elevator moved upwards.

Everything they did before has come down to in a single moment, the moment they remove Cipher from Orre. The moment to take their land from darkness. The moment they permanently liberate the Shadow Pokemon from the darkness. And most importantly, the moment to save the world.

When the elevator stopped, the two trainers found themselves in a large coliseum, without any people in the stands. Cold metal lined the entire room and sorrow whispered in the wind. The sorrow of the Shadow Pokemon that lingered long after their hearts were sealed filled the room.

A short, old man stood in front of them, as though he was waiting for this moment to come. On his face was a smile, not of joy and happiness, but of malicious intent. "So glad you could make it," he said in a sinister voice.

"Greevil, or should I say Mr. Verich?" cried Michael, "It ends now! Today, we shall defeat you and your XD001 I don't know what Pokemon it is, but it will surely fall!" Jovi took pride in the fact that Michael was the one saying this, most of the time he was a carefree and happy person. But when it came to Shadow Pokemon, Michael seemed as though he was replaced with a person who didn't understand giving up, and sometimes mercy. Jovi, of all people, should know, they were bother and sister after all.

Shadow Pokemon are Pokemon that have had their hearts sealed by twisted science. They were cold and heartless creatures that were infused with dark energies and hatred. They used attacks infused with dark energy. They were incapable of understanding mercy and honor. All they knew was to fight. They were fighting machines, nothing more, nothing less. Showing a Shadow Pokemon with kindness and friend ship then purifying it was the only way to save a Shadow Pokemon.

But Cipher was planning to create what was called an XD Shadow, a supposedly impossible to purify Shadow Pokemon. It was the plan for the ultimate killing machine, with little hope to defeat. Stopping the development of these Pokemon was the sole reason why Michael and Jovi set out to defeat Cipher.

Jovi snapped back to reality as she ordered Plusle and Minun into battle, while Michael released his Espeon and Flygon from their Pokeballs and sent him into battle.

"Normally four against one is an unfair fight," Greevil laughed, "but you will be fighting the soon to be Father figure of all Shadow Pokemon. Fight him if you dare! Come forth, XD001, Shadow Lugia." Greevil declared. The Coliseum around them seemed to open up, revealing a black winged creature coming towards them. A birds like silhouette entered the arena, striking a thunder clap of fear. Its wings and body were black from head to toe, except for the vicious red eyes and the white belly. "After this, your Pokemon shall become excellent Shadow Pokemon and will look up to XD001. Shadow Lugia, I command you to use Shadow Blast on them." The Shadow Pokemon didn't hesitate, not out of loyalty, but out of lack of free will, and fired a vacuum of darkness at Michael and Jovi's Pokemon.

"Jovi thinks this is bad," Jovi told her bother. "Plusle, Minun, Double Helping Hand on Espeon!" When ever Jovi does not talk in third person, she's serious. The two electric-types quickly had hold of Espeon and stared at the powerful vacuum attack.

"Espeon, Hyper Beam!" Michael ordered. An ethereal glow surrounded the fox, giving it an almost other world appearance. Espeon launched a beam of seer toward the vacuum and the attacks collided, causing sparks to fly.

Helping hand was and attack which helped support another attack. But the Hyper Beam barely held out against Shadow Lugia's Shadow Blast, even with two Helping Hands. Although the beam wasn't strong enough to bypass the Shadow Blast, Shadow Lugia distracted enough for a clean shot. "Now, Flygon take Shadow Lugia down with a Double-Edge!"

While the beam attacks were still firing, Flygon rammed into Shadow Lugia, causing it to cancel its Shadow Blast attack. Flygon quickly escaped, before the Double Helping hand/Hyperbeam combo cut its way towards Shadow Lugia. The attack caused heavy damage and knocking darkling into. "Jovi, now's our chance!" Michael used his left arm to charge up a Snag Ball, a Pokeball designed to capture trainer owned Pokemon. He threw the Snag Ball at Shadow Lugia, but it was blocked by a huge stone. "Huh?"

"Jovi sees more Pokemon." Jovi told her bother, noticing there way a Rhydon, Tauros, and Exeggutor standing before them. "Jovi thinks Battle is in Michael and Jovi's hands..."

"You will not snag my precious Shadow Lugia!" Greevil declared. The Shadow Pokemon acted as a blockade between the Snaggers and Shadow Lugia.

"Let's take care of these guys first Jovi." Michael told his sister, his Aura Reader going haywire. While Michael took out a few potions and Pokeballs, Jovi sprayed a few Potions on their injured Pokemon.

"Michael right, we snag Lugia last."

Thirty minutes later, Rydon was finally snagged, along with Exeggurtor and Tauros. The tough battle took its toll on Espeon, Flygon, Plusle, and Minun. Jovi and Michael were at the ends of their wits seeing their Pokemon suffer greatly in battle. The poor creatures were acting as self sacrifices to end the terror that is Cipher. Shadow Lugia was still knocked out, but Greevil slipped in a revive to make it conscious again.

When Shadow Lugia was revived, a program in its brain told it to leave the battle, an anti-theft action to prevent snagging. Shadow Lugia departed from the battle and flew towards the sea, heading for another place where Cipher existed. "We will meet again, boy!" Greevil said as a helicopter flew behind him. The old man climbed into the flying machine and disappeared along with Shadow Lugia.

Recalling their pokemon left Michael and Jovi alone, or so they thought. They didn't realize it, but they were being watched. A man with red hair and a blood, red cloak stood before them. "Well played, but your battle isn't over." He said.

"Ardos? We didn't come here to fight you." Michael told the man.

Jovi gave a gasp. "Michael and Jovi already beat you!"

"Nor will you have to again. I have no Shadow Pokemon, but I bring news," Ardos told them. "Grand Master Greevil has left to Kanto to create more Shadow Pokemon. From there, he and an allied organization, Team Rocket, shall a mass a great force. A force that I no longer have any intention of joining." The cloaked man then stepped back, planning to hide in the shadows of the coliseum.

"Why should Jovi or Michael listen to bad man?" Jovi told the former Cipher admin.

Ardos sighed. "Because, I want my father back..." he said as he was completely engulfed by the darkness. Michael and Jovi nodded and took another elevator out of headquarters. When the made their way down, they found the Robo-Kyogre and left Citidark Isle. But they didn't realize Ardos was still watching them as he said to himself. "And I know both of you do also..."

* * *

Jovi and Michael stood before their mother and Professor Krane, the heads of the Pokemon HQ of Orre. Their top concern was Shadow Pokemon and how to stop them. After hearing of the events that took place in Citidark Isle, their mother gave them a tight hug. They were relieved when they heard Cipher left Orre, but was shocked to know where Greevil was heading. If Cipher or Team Rocket gained more Shadow Pokemon, it could spell trouble.

"Well, I'm glad to see you two are alright." Krane told the children. "You two will have to track Greevil down, before he controls more Shadow Pokemon. I better activate more snag machines, we'll need all the Snaggers we can get." Krane walked away, returning to his lab work

Michael was relieved that they could rest for a bit, he and Jovi practically went cross-country through Orre, battling Cipher nonstop. But his primary concern was not about himself or Jovi, but rather their Pokemon. They were heavily battered and injured in the battle and the moment they returned to Pokemon HQ, they were admitted into the Emergency Room. "How are our Pokemon?"

"You may see them if you'ld like." Their mother, Lily, told them. Michael and Jovi spilt up and turned to their respective Pokemon. Michael to Espeon and Flygon; Jovi to Plusle and Minun.

"You both did good today, I'm glad we did at least drive Cipher out of Orre." Michael told his Pokemon.

Espeon told Michael with his Psychic powers. "WE failed, Greevil got away!"

"It's our fault there will be more Shadow Pokemon..." Flygon said to his trainer, using the aid of Espeon's mental abilities.

"Well, then we're just going to have to do better this time." Michael told his Pokemon. "If we worry about it, yet do nothing, we will fail. But if we work hard enough, we will win and Cipher will be another name in the dust. Tomorrow, we sail to Kanto and make sure Cipher loses this time." Both Pokemon gave a silent smile to their trainer, both knowing he was right.

* * *

Max was excited about today. Today was his chance to finally have a Pokemon. He cheered as he leapt out of a guest bed in the Ketchum home. Normally Max would have received his license from Professor Birch, but he wasn't in Hoenn at the moment. Normally something like this would have annoyed the boy to no end. But then Max realized that none other than Professor Samuel Oak would present him with a Pokemon. He craved such an honor such as this the moment he heard the word "Pokemon".

Although he was too young to be a full-fledged trainer, he was old enough to be an apprentice. Apprentice trainers were a recently added concept that allowed kids a year from receiving a full license to start training Pokemon. An apprentice would have to stay and learn with his/her master and both must have a good amount of responsibility. An apprentice could not participate in Gym battles also, but can still capture some wild Pokemon. All of these conditions were acceptable to Max, considering he was still going to get a Pokemon and the word "trainer" appealed to him. Then there was his master to be, Ash Ketchum.

After the events that took place yesterday, Ash agreed to teach Max how to train Pokemon. Even though Max knew a lot about Pokemon, he didn't have much experience to use such knowledge. He was still confused to learn that a lot of the stuff he studied was able to be proved wrong.

Max slowly made his way to the ground floor, noting that his traveling companions were temporarily grounded, due to a supposedly missing Gym leader. Good news was that the Elite Four, the toughest trainers in a country, have sent one of their own to fill the missing place, so things can get back to normal (if there was ever a normal in their world).

Brock, the former Gym Leader of Pewter City, was a tan skinned and squinty eyed fellow with a desire to be one of the best breeders in history. He had a tendency to ask every cute girl out on a date and get rejected in a matter of five minutes(sometimes even seconds). Being a used to rock- and steel-types, Brock's Pokemon were usually defenders.

May, Max's sister, was busy thinking of new ways to train her Pokemon in contests and some fighting skills. Her Pokemon were Combusken, Munchlax, and Bulbasaur, which apparently had taken a liking to Ash's. Her battle and contest style was based on images and graceful movements. Although she was sometimes a bit crazy, she tended to be nice.

Misty, the once Gym Leader of Cerulean City, had decided once again to travel with Ash. Apparently, Brock's mother, Lola, who had once tried to make Pewter Gym into a water arena, decided to take over for a while. It could be said she loved water Pokemon with a fiery passion, if those the words weren't contradictory to each other. She had a tendency to hit who ever made her angry.

The Go-Getters weren't Pokemon trainers, rather they were Pokemon. They came from an island some miles south of Pallet, which was completely inhabited by Pokemon. Because this island was plagued by natural disasters, the inhabitants formed organized search parties called Pokemon Rescue Teams. Of these teams, Team Go-Getters was one of the oddest.

Maganuim, team leader, was related to Ash's Bayleef. She, unlike most others grass-types, who were usually passive and submissive, often took charge of the team. Back on the island, she leader her team through various places, including lava and deserts, and if the need arose, organized multi-team missions.

Charmeleon was easily the tamest, yet the most vicious, the most easily scared, yet bravest charmeleon in existence. Most of the time, he acts tame and plasters a smile on his face (plain unusual on a charmeleon if you ask me). Other times, he bursts into a rage that could scare the charzard of Team A.C.T. He was scared of some humans and had a paraniod fear some human would take him away from his friends. But if his friends, who included some humans, were in danger, he forgot the meaning of the word "fear". All of these behaviors were things a charmander would do which make it seem his brain refused to grow up.

Wartortle wasn't exactly your normal pokemon either, he was once a human. One day he woke up as and squirtle joined team Go-Getters as the medic. He helps his team mates by storing and managing all of the items he keeps.

Finally, Ash Ketchum, one-day owner of they house they were lodged in, soon to be Max's Master, and big dreamer, was still rubbing the eyes from his sleep. He had a miniature army of Pokemon at his disposal and knew their skills and abilities very well. His main Pokemon, Pikachu, usually was somewhere on his shoulders. Ash and Pikachu's encounters were with numerous people, most of whom were successful in their fields of work.

Max looked at his friends, all of whom were Pokemon trainers (or Pokemon in some cases) in someway, soon he would be one aswell. Max soon stepped closer to a nearby clock and gave a gasp. He quickly ran out the door, forgetting he was still wearing pajamas. On the clock it read 10:51

"De ja vu, huh, Pikachu?" Ash told his starter.

Pikachu giggled like a child as he told his trainer, "Just like you...He really would make a good apprentice, he even got late on the same time. I wonder what Pokemon he'll get..."

"I believe it wouldn't be one of the starters. Knowing Professor Oak, I think he already got a special Pokemon for him. We should be moving out soon as he gets it/he/she..."

At this, Team Go-Getters decided to make an exit for a while. "We'll get ready." Wartortle told the humans.

Max was scared. Not only he was going to get a Pokemon, he was going to receive it from Professor Oak. He took deep breaths and slowly made his way into the laboratory. He was soon standing face to face with Professor Oak and what looked to be a table holding three Pokeballs.

"Ah, Max so good of you to come..."Samuel Oak told the boy."I would tell you to choose a Pokemon, but well see for yourself." He directed Max to the table and he began opening the Pokeballs, to find them empty. Max started to seem like he had lost all hope, but Oak couldn't let the boy down that easily. He always kept a few extra Pokemon especially for kids who wake up late. "Wait just a second." Professor Oak pushed a button on his computer and a fourth Pokeball appeared on the table. Max slowly walked up to the table once more and grabbed the Pokeball. "I always carry a few extras, just incase."

Max gleefully opened the ball releasing a strange creature with a blue, bell shaped body and a single red eye. "Beldum..." it said.

"Wow a Beldum!" Max said awestricken. The Pokemon Max was staring at was deemed highly intelligent when evolved. And if there was anything Max valued, it was knowledge.

An hour later, Max and Beldum came returned to Ash's house. The pair rang the door bell, which Ash, being one of the people who lived in the house, answered. Both Ash and Pikachu were just weirded out when they saw Max and his new Pokemon, beaten and bruised. "Uh what happened?" Ash asked.

"Uh Beldum and I tried battling one of the nearby Spearow and then a huge flock came by and attacked. Then Beldum came using Take-Down all over the place. We kind of broke a bike, good thing the owner wasn't there..."Max said with worry. Ash and Pikachu just seemed startled that the boy had a first day almost exactly like that of their own.

Misty, while over hearing the conversation between the now master and student, slapped herself. She forgot to take her bike with her into Pallet Town, now it's broken, again. Was the world out to get her and her bike?


	2. Many Secrets

A/N: I've got the weirdest idea for what Wartortle's former life was like. Also, using a few maps from the old games, I pinpointed Orre's possition to be some where north-west of Johto.

For those of you who don't know what an apprentice system is here is a Pokemon trainer's version

Apprentice...Trainer...Master

This was based off of an old class system that is still used today, ussually in hands on training jobs. I thought it would be good to add this because it's good enough grounds to make a nine year-old have a Pokemon. Have you ever noticed in Gold/Silver/Crystal that there are kids you have to battle that were 7 or 8? Well, this gives enough grounds for them to do so.

* * *

Delia Ketchum stood in the kitchen, work to distract herself from what was going to happen today. Ash was leaving and it wasn't in her heart to stop him. No, he was a big boy and needed to make his own decisions. Besides, he's a Master and he has a student, he certainly can't to rigorous training in a town! So now, the weeping mother had at least made sure to see him off, he may never come back in a whole year. That thought made her cry... 

Atleast until Mimey, the Mr. Mime had to say something about it. _"Cheer up, Delia! The boy needs to explore the world and make something of himself. Also, don't forget he's involved with saving the world now and again." _The mime told her. Although she would never tell her son, Delia was a pokemon trainer herself, having experiance from being in the neighborhood of Prosfessor Oak and having a son who made a record most couldn't match. Mimey may be a good choreboy, but an even better battler. _"Who knows, he maybe on the trip to becoming a master as we speak." _Mimey gave a laugh_. "He's even got his own apprentice, in my book, that's got to be a major responiblity."_

Delia sighed. She knew the Mr. Mime was right, she just wondered how her son felt and wished she could be with him more. But it was now time to let go, again. "T-thank you..." She said to her only Pokemon. And her only companion when her son is out traveling...

* * *

Max and Beldum could not believe what they just heard. Ash and Pikachu spent an hour telling them about their first day. How they met, how they met Misty, and most importantly, the bike! Max had told Ash that the bike had a pair of fishing rods and was parked near a stream. The only person who would do that was...Misty! Ash tried to keep his head cool as the Former Gym Leader made her appearance between him and Max. Appartently, she over heard her bike being destroyed again... 

"I think I know who the bike belongs too..."Misty started with a hint irritation in her voice. As she made her way towards Max, Ash stepped in and tried to hold her back. Max could only stare at his new master stand between him and a world of hurt.

"Uh Misty wait..." Ash started, "Uh...If anyone's is to blame it shall be me." The room suddenly went cold and Pikachu wanted to know if a certain "bad" place froze over. Ash taking responsibility for anything was as rare as seeing a legendary on your first day as a trainer. Then again Ash and Pikachu did see Ho-oh fly past them on their first day. Ash spoke again, struggling for words to help him. "Uh...as Max's master...Uh...and I take full responsibilty for his actions..." Max hoped this would not be his master's last stand.

Misty looked closely at Ash to see if anyone replaced him or it was April Fool's Day. Neither were true. She gave a sigh before saying. "Ash...I wasn't going to punish him..." _After all, he's just a kid and I joined Ash because I had nothing better to do. _To the relief of Ash, Pikachu, Max, and Beldum, that was load of their minds. "But someone still has to pay for my bike..."She frowned a bit.

Ash dug into his pockets and found a small coupon. it read: "Free Bike Repair, no matter how damaged and valid at any Bike store in Hoenn, Johto, or Kanto." Ash gave a gulp hoping the coupon would work. "I asked Mom to get some of these for me, since I have this tendancy to dstroy bikes...I thought it would be best to keep some arround incase I destroy more..." Ash chuckled at his own failures.

"Well, I'm glad you finally know how to be responsible Ash. That was unexpected." The former Gym Leader giggled, taking the coupon from Ash's hands. "But remember this too boys...I'm still coming with you." she said as she parted with them.

Ash decided it was best for a simple lecture, which for Ash was rare."Now Max I know you know _alot_," said Ash to his student. "But knowing something isn't the best thing to fall back upon. You still need _experiance _and the _heart_ to fight. If you didn't have the heart to do what is needed to be done, your knowledge will useless." Ash stated. Max just stared at Ash, it seemed he was full of surprizes today. Even though he knew Ash for a year, he never knew Ash could make a lecture that could be worthy of Elite Four. Then Ash even went as far as to insult his inteligence. Max was a bit angry, but he knew Ash was right. Even if he knew everything, that knowledge would be useless if he couldn't employ it.

Ash inhalded and exhaled, clearing his mind to think."Okay, first off I need you to work on your basic attacks. I need you to evalute Beldum by seeing how strong it's Take down attack is by seeing how fast it moves. Then, you need to practice it, okay?" Ash told his student. Max nodded.

After an hour, Max examined the recoil effects of Take Down on his Beldum. The blue steel-/psychic-type was determined to make a good impression, but in the end tried itself out. Beldum slowly made its way to Max, hoping it didn't disappoint its trainer. Max rubbed his Pokemon's head, or atleast what he thought was its head, and told it, "There, there, you did your best, everyone get tired at some point or another. We should get back, I can't wait to show you to the others" He rubbed his stomache, feeling hunger. "And I think it's lunch time."

"Yeah and we should be leaving soon, I can hardly wait to battle someone!" Ash declared, Max couldn't help but think the same thing.

* * *

Wartortle, of Team Go-Getters, certainly wasn't your average Pokemon for two very specific reasons. The first one, he was part of a Pokemon Rescue Team, which was strange on its own. He and his teammates and friends, Charmeleon and Meganuim, were currently assigned on a long term mission to protect Ash Ketchum of Pallet Town. They have no idea why, but they believe it has something to do with the fact he saved several Legendaries and the planet on numerous occasions. 

The second reason Wartortle was different was because he really wasn't a Pokemon, four years ago, he was once human. He doesn't remember how or why,but he turned into a Squirtle and lost most of his memories. Then he met Charmander and Chikorita and joined Team Go-Getters in order to find a place to belong. Over time, he decided he was happy the way he was now and decided to stay with them. After several years, they evolved into the forms they now had. But they still wondered about Wartortle's origins among other things. One day, they received a letter telling them to stop a de-evolution beam, that's when they met Ash and his gang. In the end, they were successful, but they wished they could stay for a while longer. Captain Poliwrath gave them orders to do so, but inexchange they must protect Ash, which they have no problem over.

Wartortle slapped himself, for day dreaming. He was supposed to be packing his rescue kit full of items. He made an inventory check on the yellow and pink box. He found approximately five Oran Berries, a few Rawst Berries (incase of a certain fire-type lizard), and most importantly, an old TM Case. Wartortle found the TM case when he was exploring one of the dungeons arround Pokemon Square and used it to keep any of those fragile disks safe.

Wartortle almost slapped himself again, but was stopped by the first friend in his life. If there was any thing Wartortle knew, it was theat Charmeleon was his first firend. _"Hey, chill out," _the lizard told him, which sounded weird for the obvious reasons,

_"Why are you beating yourself up?" _Meganium asked.

_"Because, I'm suposed to focus here,"_ Wartrotle told his friends. _"we have work to do, and I really need to figure a fewthings out. I'll see you both at Ash's house."_

The other two Pokemon waved goodbyes as Wartortle made his way into Professor Oak's labratory. Tracey was preparing to open bags of Pokefood, as a certain meal time was coming soon. Wartortle moved closer to the research assistant, hoping he could answer a few questions. "Wart Wartortle...?" What just happened? He could speak in human when humans were arround, but he can't speak to to humans right now. Then the answer hit him, he only spoke human when Ash and Misty were arround. But why? Looks like he had another mystery on his hands.

Tracey was just as confused, they heard Wartortle speak in perfect human, even better than Meowth's! But right now he couldn't. "Are you okay?" Tracey asked. Wartortle nodded. "I heard you speaking human yesterday, but not now. Do you know why?" Wartortle shook his head. "Well, um...I'll see you guys at Ash house then?" Wartortle nodded and walked out the door.

* * *

Michael and Jovi stood side by side, wondering what Aldos said to them. The pair decided that they would have to track Greevil down in Kanto, but from what they knew, Kanto was pretty large and it could take weeks before they even know where Cipher was. They also relised there were many agents from Team Rocket and many of them had good ammounts of experiance and even greater funds than Greevil ever had. The brother-and-sister-duo sighed, this wasn't going to be easy. 

"Looks like we've got our work cut out for us. The two of us have only two Pokemon, so that's four altogether. I really wish, we never gave away all of the ones we snagged from Cpiher, yet." Michael told his sister. Right before they fought Greevil, Michael told the Pokemon HQ to give out all the purified Pokemon. This was done to make sure the Pokemon had good homes. He couldn't just take them back, that would be rude!

Jovi giggled. "Michael forget Kanto has many, many Pokemon, we can catch with out Snag-machines and Aura Readers." Jovi told her brother.

Michael thought for a momment, remembering the first time he caught a wold Pokemon. He remembered when he spotted a Trapinch and battled it with his Eevee. He also remembered how fun and easy the capture was because it wasn't a shadow Pokemon. Sicne that moment on, the two became his headliners and powerful additions to his team.

Returnering back to reality, Michael then remembered the standard trainer's rule of six pokemon per person and the customary single battle rule that is in action everywhere, but Orre. He sighed, trying to think if there was anyway he could take down an organization. "Jovi," the red head said, "we still can't take down Cipher all by ourselves and we'll need more manpower to do it. So have any ideas where we can get more help?"

* * *

Unknown to Michael or Jovi, Professor Krane, Head Researcher of Pokemon HQ in Orre, was listening to their conversation. They were right, they can't take down Cipher by themselves. When they tried it the first time arround, Cipher greatly underestimated the battling skills of both Michael and Jovi, thinking that kids couldn't stop them. Now they were fully aware of their might and wouldn't hold back out of pride. 

Professor Krane needed more snaggers, good ones. He tried to think of any one he knew that had well experianced trainers, then the realization hit him. If there was anyone who knew who were the strongest trainers, it was Professor Sammuel Oak of Pallet Town, Kanto. Oak lived very close to where has Cipher relocated and was once Krane's teacher, so he was the perfect man for the job. Krane made his way to the video phone and dialed the number his former teacher used. There was a moment of silence before an aged man appeared on the monitor. "Hello, Professor Oak, it's me Krane."

Oak examined Krane, looking to see if he was telling the truth. He nodded and said, "Ah yes, Krane, it's been a while. I hear you now live in Orre, working on the Anti-Shadow Pokemon Movement. How does it go?"

"Cipher moved out of Orre...But into...Kanto..." Krane told his mentor, no matte how much he didn't want to.

Professor Oak frowned."I figured this much. Yesterday, several trainers told me of an incident where they battled these "Shadow Pokemon". I believe the Cipher has joined forces with Team Rocket. I have several good trainers, but they should be leaving today. But I think they'll leave tommorrow, if I tell them about Cipher. It's lunch time, so I know where they're at."

"You better try to stall them, I'll get more Snag Machines and Aura Readers ready." Professor Krane said to his former teacher, before hanging up the phone.

* * *

Michael and Jovi were outside of the Pokemone HQ in Orre, waiting for their Pokemon. Sure enough, the Pokemon finally left the Emergency Room of the labratory. The two trainers greeted their Pokemon as they ran towards them in open arms. "Espeon! Flygon!" Michael cried as his two best Pokemon ran toward him. 

"Plusle! Minun!" Jovi cried, hugging her two companions. She began petting and hugging them in the most painful way possible. She was after all someone who didn't know her own strength. What was even more surprising is the fact Plusle and Minun liked it! "Jovi soo happy!" She cried, talking to herself in third person again.

"Glad, you're alright guys." Michael told them.

_"Like we'd be taken out be a darkness empowered Lugia!"_ Espeon used his psychic powers to communicate and allowed the humans to understand what the Pokemon were saying, His vioce carried much arrogance, he seemed unfazed by the fact he almost got crushed by a Shadow Blast.

"Good to see near death experiances don't make you freeful." Michael told.

Flygon just sighed, "Honestly, I can't wait for a rematch. Michael, do you know where Cipher went?"

"Kanto..." Michael started to say," but we need more manpower to take down Cipher. But who?"

"I believe I can answer that." Everyone turned their attention to Professor Krane, holding a breifcase. "Michael, Jovi, you tow must go to Pallet Town in Kanto and meet Professor Oak. He is trying his best to hold off some strong trainers from leaving Pallet too soon." He threw Michael the breif case. "Michael, these are more Snag Machines for the trainers. You and Jovi should ride Flygon. His speed is almost that of a Dragonite's, so he could take you there in four hours." He took Michael's PDA and inserted a disk in it. "I've upgraded it with Kanto's map, best of luck to both of you." Krane said as he turned

"Thank you." Michael said, then turned his attention to Espeon. "Espeon, I'm sorry I have to do this." He said as he pulled the fox's Pokeball.

"No need." were the last words of the Psychic, before he was tucked away in a red and white ball.

Jovi hessitated, but managed to put Plusle and Minun in their balls. "Jovi sorry!" She cried.

"Flygon, we better get going. Jovi come on!" Michael called as he and Jovi climbed the dragon-/ground-type. They soon took off, heading southeast, bound for the hamlet of Pallet Town, Kanto.

* * *

To those of you who don't know, Flygon and Vibrava are two of the few Pokemon that can learn Fly, with out having flying-type traits. Read the Pokedex for more info. 

Also the hours of peace are coming to a close, as the battles will soon come.


	3. Lunch

Michael, Flygon, and Jovi were flying through the air at high speed. The trainers had to keep their Pokemon in the Pokeballs to lessen Flygon's work load. Clutched in Jovi's hands was the briefcase containing the extra Snag Machines. The little girl was struggling not to let go of the container, as she and Michael were flying through the air. "Jovi scared..." 

Michael, even though he wouldn't admit it in front of Jovi, was scared too, but for a different reason. The high altitude and vast desserts of Orre would have made navigation a difficult task, good thing Michael had an upgraded PDA and Flygon have an internal compass. He was also worried that he may not make it in time to thwart Cipher. He said, "Don't be afraid, Sis. We'll be okay and make sure Cipher falls, this time. "Jovi gave a whimper, but soon stopped. She must have been afraid of Cipher. It's no surprise, most little girls like Jovi couldn't handle seeing Pokemon being turned into fighting machines.

Michael found himself thinking back to when he first saw a Shadow Pokemon. The fear he felt when he saw that Teddiursa with its eyes full of hate and the aura darkness. He shuddered to think what it felt like, being a slave of darkness. He vowed to make Cipher pay for their crimes, one hundred fold! He then turned his attention to Shadow Lugia. He remembered that the Shadow aura that surrounded that Pokemon was so strong that its skin turned black. When he told Professor Krane that Cipher caught a Lugia and managed to Shadow it, the poor doctor almost fainted. Michael knew that this was for a good reason, catching a Lugia taken a lot of guts, but Shadowing it must have took at least several "wills of iron" (if that's even possible) and pure cruelty.

Michael just realized he and Jovi were now flying near the edge of Orre and quickly snapped himself out of his mid-flight daydreams. Both brother and sister noted that they were flying over a dense forest, filled with wild Pokemon. He activated his PDA and examined his location. The machine read: "Johto, Ecruteak City". Jovi tugged on her brother's shoulder while pointing with her fingers.

"Look Michael! Look! Jovi found big towers!" The girl cried. Michael turned his attention to the two towers Jovi found. They were definitely both made of wood and seemed to have a traditional feel, something that was uncommon in the dessert. Back in Orre, most of the buildings were made of metal and concrete, and most of them were made just a few years ago. But these stood strong for hundreds of years. One tower was burned and ruined beyond repair, the other looked brand new. Michael smiled at the sight, knowing that these were just many of the new things they'll be seeing in their new journey.

* * *

Wartortle decided to ask Misty a few questions, hopefully ones that the human girl would understand. As he made his way toward the Ketchum home, he noted that Misty was pulling what looked like the remains of a bike. If you could call it that...The handles and frame were smashed to pieces, it seemed like something did The human-turned-Pokemon decided to silently walk up to her and slowly made him known. That was the plan, but the girl spotted him. 

"Before you ask," Misty started. "Max inherited the ability to destroy bikes. I swear, Ash seems to be a curse to all bikes." This caused both of them to laugh. "Is there anything else you need?"

"War? Tole?" the human-turned-Pokemon tried to speak in human. _Why is it that I can only speak human when Ash is around?_ He blushed and slowly backed away.

"Huh? Is something the matter?" Misty asked. She knew Wartortle could speak human, but why not now? "Can't you speak human?" Wartortle shook his head. "Do you think there's a reason why you can't speak human now?" Wartortle shrugged. "Well, I guess I'll see you at lunch." The girl said as the Pokemon walked in the house.

* * *

Wartortle entered the Ketchum household, planning to meet with Delia Ketchum. Wartortle was never formally introduced to Delia (or at all for that matter), so he figured it would be good manners to meet with her. When he made his way into the kitchen, the Pokemon saw a particularly helpful Mr. Mime and whom he believed to be Ash' mother. The two were cutting vegetables, mixing spices, and boiling water, the obvious combination for making a soup. _How do I know they're making soup?_ The former human asked himself. 

"Come on, Mimey, lunch is in about an hour." Delia Ketchum called.

Mimey made no hesitation to increase his efforts by chopping potatoes at the speed of light (not a reference to Team Rocket) with the exact precision of master chef. _"Ya' got it!" _The mine declared. As soon as the mime finished, he turned his attention toward Wartortle. _"Hey, are you this Wartortle Ash told us about?"_

_So Ash told Mimey and Mrs. Ketchum about me? What else did he say? _"Uh...yes!"_ Huh? I can speak human now?_

Delia made it known that she was paying attention. "A wartortle who could speak human? I thought a talking Meowth was weird." She giggled for a bit. "So how did you learn?"

Wartortle sighed, knowing that Ash at least kept some secrets. "I don't know myself." _I really don't want her to worry._.

"I guess I can." Wartortle said. He carefully added a few teaspoons of salt, pepper, and other spices, unsure of how he knew how to measure them. He silently hoped that the spices he added didn't spoil the food.

_"Can you help with lunch?" _Mimey asked

Wartortle's mind was swimming with questions. What was the difference in each of his conversations with humans? Why does his language shift because of that? All the human-turned Pokemon hoped is the answer is something he wouldn't regret.

* * *

Ash and Max were finally heading back to the house. After a hard morning's worth of training, the two were ready to start a new journey on the road, League Tournament or not! This lunch was hopefully going to be a farewell party. The master and apprentice slowly pushed open the wooden door, making their way into the kitchen. The other travelers were already there, waiting for the student and teacher duo. A nearby table held several bowls of soup. 

"Ash! Max! You guys are late for you own farewell party." Brock said.

"Hey Brock, I guess this is a farewell meal huh?"

"You said it." the Rock-type Gym Leader replied. Ash hastily grabbed the nearest bowl of soup and wolfed it down like he hadn't eaten in weeks. Pikachu grabbed a few bottles of ketchup and drank their contents. Beldum copied its master by putting its mouth (or at least what looked like a mouth) close to a ketchup bottle

Misty cracked a smile. "It'll feel good to be on the open road again...I wonder if I should do more than just walk all day, like do Gym battles, it would be ironic though, since I was a former Gym Leader."

"Maybe you should take part in some Pokemon contests with me. Then, you'll be my only rival, other than Drew, who isn't out for my blood!" May commented. She was happy for once that she wouldn't be the only girl on this trip anymore. Both of them laughed.

_"Hey Wartortle!" _An extremely excited Charmeleon called.

Meganuim, leader of Team Go-Getters, told her teammate, _"We were waiting for you."_

"Hey guys!" Wartortle said, noting that he was still speaking human. It was possible there was a reason for this shift and he was going to find out.

_"Where were you?" _Meganuim asked.

"Fixing lunch, Mrs. Ketchum asked me to." Wartortle replied.

Thinking quickly, Charmeleon grabbed one of the bowls of soup. After smelling it to make sure it wasn't poisonous, he devoured the soup, in a manner unlike that of Ash. _"Wow! Where did you learn to cook? You never once cooked food when were in Pokemon Square."_

Thinking Charmeleon must have been sarcastic or he lost what ever taste buds he had it a fire attack, Wartortle grabbed another bowl and tasted the soup for himself. And it actually tasted good! Wartortle wasn't sure where he learned how to cook himself, it wasn't instinctual, and so he must have learned as a human. _One of the many questions I may never answer._

Max sat alone, listening to the conversations. Being the only kid, he never had many people around his age to talk to. He silently hoped that he would meet someone that he could be with. Even though he was now an apprentice, he wasn't a trainer just yet.

* * *

An hour passed and the gang was all set to go. Their bellies were full and their Pokemon were healed. Ash decided to bring his starter Pikachu, Growvile, and Phanphy. May was coming with Combusken and Munchlax, many because her Bulbasaur was staying at the lab. Brock brought Fortress and Mudkip. Misty had Corsola, Politoed, and Azurill. Max had only one Pokemon, Beldum and a few empty Pokeballs, which he hoped to fill in really soon. 

The gang almost left the kitchen if they weren't blocked by none other than Professor Oak. "Come to my lab," he said. "There are a few things we need to talk about." And so, the gang followed the old man into his laboratory.

"Uh...Professor Oak, is there something wrong?" Ash asked.

Professor Oak sighed. "Indeed something is wrong. Do you remember the events yesterday; Pikachu was turned into a Pichu?"

_"You don't have to remind me." _The electric mouse said, not wanting to relive such an embarrassing moment in his life.

"During the raid, you said you encountered strange Pokemon who used attacks that used dark energies?" Oak said as the group nodded. "These are Shadow Pokemon, Pokemon with their hearts artificially closed off and charged by dark energy. The only group that has access to these is Cipher of Orre.

"Five years ago, Cipher and Team Snagem started what is now called the Shadow Incident. They used these Shadow Pokemon to dominate Orre. Then out of the blue, one of the members of Team Snagem revolted and attacked both Cipher and Team Snagem. He used a device called a Snag Machine to capture Shadow Pokemon from the gang members and used a statue called the Relic Stone to purify them, while a girl used her powers to see what Pokemon were Shadows and what weren't. He and the girl were responsible for the capture of one of Cipher's leaders, Evice. We don't know what happened to the heroes, but their deeds didn't go unnoticed.

"And now, Cipher has risen again and two more people taken up the mantle as "Snaggers", Pokemon trainers who snag and purify Shadow Pokemon. I am against stealing, but I am more against 'Shadowing' of Pokemon, so I can't say the Snag Machine is not needed. A room called a Purify Chamber is used to speed up the purification of Pokemon along with the relic stone. One of my former students is responsible for the creation of these projects.

"He told me that his Snaggers have been able to defeat Cipher in Orre, but now there is another problem. Cipher has left Orre, but moved into Kanto and now works with Team Rocket. But that's not the worst of the news. Ash do you remember Lugia?"

Ash would never forget that Legendary, not ever. He helped Lugia saved the world after all and also a younger Lugia in Orange Islands. "Yeah, what does Cipher have to do with Lugia?"

"Professor Krane has confirmed Lugia has been Shadowed. From all he gathered from Cipher, he says there is a chance Lugia may never be purified. Cipher calls this particular Shadow Pokemon XD001."

Ash was stunned. He felt an empty feeling is heart. He felt as though one of his friends has died and he only just found out. Brock, May, and Max never met Lugia, so they didn't understand the pain Ash felt. Misty knew because she was there when Lugia battled the three Legendary birds of Fire, Ice, and Lightning.

"Ash..." Professor Oak said. "Where there's a will there's a way. The Snaggers never managed to have snagged Lugia, but Krane believes we can purify him if they did. Krane also wants you and your friends to help the battle against Cipher." Professor Oak turned his attention towards the sky, noticing a Flygon making a descent. "And here are the Snaggers now."


End file.
